Push them to get their virtual done (control ligands and small libraries at the very least - big library if they want to put in extra effort) Push them to get their cloning - at the minimum, each springer should have two rounds of cloning. If they are strategic - they can do these back-to-back with some overlap. Expression and nickel purification would put them in a much better place.
Finish Reviewing their M&M Cloning in Canvas - if you have not already done so (should be done already) - see: GDrive/VDSStaff/Reviewing/PeerReviewAndMidSemesterAssesment by MENTORSandDrB See Sheet on GDrive, Use VDSstaff login - for this put comments down for improvement and give a rough score. - you will review the same people that you did for the Mid Semester Research report (Eric will make a Google Sheet f or this) - don't worry about evaluating the Peer Reviewers work on these (there are two people per - so Eric will check these)
Review their M&M Virtual in Canvas (should be completed by Tuesday night) Use tabs on GDrive sheet to switch between assignments - for this put comments down for improvement and give a rough score. - you will review the same people that you did for the Mid Semester Research report (Eric will make a Google Sheet for this) - don't worry about evaluating the Peer Reviewers' work on these (there are two people per - so Eric will check these)
Research Progress Checks (should be completed by Tuesday night) Use spreadsheet in GDrive/VDSStaff http://vdsstream.wikispaces.com/ResearchProgressF14 - only check up to Sunday Nov. 23rd (the last time they did a Wikispaces/Lab Notebook) - I copied the values from last check - update with the current information and see difference in score.
Review their M&M Expression, Purification, Characterization (should be completed by Friday night)
Thursday/Friday/Saturday - Lab Cleanup days
- they sign up for sheet on the whiteboard
- mentor signs off once done
Monday - VDS Party at Dr. B's House
ULN Interns
Faculty & External RelationsAssistant - Bridgitte
- see other sheet for tasks
VDS Class Assistant - Eric B
EVERY OTHER WEEK - on Mondays
- check that Wikispaces are done for each student (this will repeat Every other week) (Now may be moving to every 3 weeks - check schedule to verify)
---- put comments on each page
-- upload reviewing score to Google Docs spreadsheet and to Canvas
Lab Notebook (maybe every 2 week or every 3 weeks as determined by the schedule) -Done
- assign mentors to review each (use GDocs/VDSStaff/Reviewing/)
- once Priya has proofs them - upload grades to Canvas
WEEKLY TASKS
Update Hours spreadsheet - Mondays -Done
get paper sign in sheet form lab and enter hours into the spreadsheet on GDocs.
make sure the graph on Wikispaces now shows the latest week - need to update the links on the left most average column
scan sign in sheet and email to Dr. B (or just give the hard copy)
Update Mentors Schedule - ~ onThursdays- Done
create a new sheet within the existing Scheduling Mentors
call it Week XX and move it to the left.
remove all of the 'mentorVDS' blocks under each name and re-color the original colors.
get the link for the page from the 'Share' button and email out to the mentors requesting that they update their conflicts for next week. (one we have that info, we can make new mentor times)
Make New Lab Schedule for WeekX - ~ on Fridays- Done
make new sheet within existing spreadsheet and call it WeekXX
make lab time blocks for each day (put down a time - but we can revise them once you get it up there and we figure out the mentor schedule)
Journal Club reminder emails to class at large when the Journal Paper and the Questions's are posted - on Fridays
-- check the ScheduleFall14 for when Journal Club is
Few new things (093014) - Dr B
For the Hours sheet - Done
-- be sure the left most 'Week' column links to the latest week (verify that you can see the latest week on the bar graph on Wikispaces Hours page) - note Zains will always be out of order in the sheet vs Canvas.
-- Upload grades for hours in Green highlight on the Hours page to the Canvas.
ON the Wikispaces Research Pages - Done
- change the order of the link to wach students' page to be alphabetical by last name (with Springers as the first group and Vets as the second group).
- then change order of rows in the Wiki grading spreadsheet in Google Docs to match
(will be easier to review them when in order)
Upload LabNoteB grades to Canvas- Done
New things (10/06/14) - Dr. B
create assignments on Canvas for -Done
PeerRevMidSemResRep
M&M Cloning
PeerRevCloning
M&M Virtual
PeerRevVirtual
M&M ExpressPurChar
PeerRevExpPurChar
100714 - Done
Start entering names and UTEIDs of students from the Open Houses into a spreadsheet on VDSStaff GDrive
put in /Misc folder - call it OpenHouseSignInsVDSF14
The paper list is on the clipboard in the lab. Leave a few sheets there for the Friday Open House
Scan and email copies to me. Can leave originals in my mailbox or on desk.
After Friday open house, enter the rest of the names.
I will send some to the Stream Sort
10/19/14 - Week 9
Using your spreadsheet in GDocs, then upload to Canvas- Done
check to see who has PyMol Refresher done (re-check since the first round not many had turned in).
On your spreadsheet in Google Docs, Enter the date that they submitted (we can adjust grade based on days late).
Enter a Base Grade (assuming no days late)
Assign points late and upload finals to Canvas
.
Lookin GDrive/VDSclass/Results&Data/PyMolRefresher
- if assignment is there and they have the images (compare across the assignments to see what is needed), then they get a 10. If not put a '0' or a fraction of the grade based upon what is missing. I will check the fractional ones.
VETS - should be completed already
SPRINGERS - should be completed already
Using your spreadsheet in GDocs, then upload to Canvas- Done
check to see who has Virtual Screening Refresher done
Make a grade column in Canvas.
Lookin GDrive/VDSclass/Results&Data/VirtualScreeningRefresher
- if assignment is there and they have the Tables and images (compare across the assignments to see what is needed), then they get a 10. If not put a '0' or a fraction of the grade based upon what is missing. I will check the fractional ones.
On your spreadsheet in Google Docs, Enter the date that they submitted (we can adjust grade based on days late).
Enter a Base Grade (assuming no days late)
Assign points late and upload finals to Canvas
VETS - should be completed already
SPRINGERS - check at beginning of next week (Week10)
Upload LabNotebook C grades to Canvas- Done
Check Wikispaces for Week 5,6,7- Done
-- see Schedule for due date
-- upload to Canvas (change grade name in Canvas to be Wiki5,6,7)
Upload grade to Canvas for Target Page Grade- Done
Add sheet for pLIC Cloning Exercise to one of your spreadsheets - Done
- just needs to be graded for completeness (i.e. full credit if all there, or partial for most, or none if missing)
- upload to Canvas
10/23/14
Schedule an Enzyme Assay Meeting with some of the Veterans and Dr. B (and Vicky and Anita)- Done
-- Primary people: Luis, Nikki, Andee, Cidia, Charina, Andrei, Hailey
-------------Secondary People: Zain, Carolyn, Xenia (Brianna), Christ T
-- check students schedules and Dr. Bs
-- shoot for Monday afternoon (~11:30 or 12?) - verify with Dr. B
--- send out email to those people
Modify Grades -Done
-- Monica Li for pLIC cloning exercise - gets a 10 -Done
-- Snaiya Hirani - PyMol Refresher - gets grade according to the date it was created (I think she did it on time - but just had it in her Student folder instead of PyMol Refresher folder)- Done
Create new GDrive spreadsheet in VDSStaff/Reviewing for the Mentors to do Peer Review assessment - Done
- should have a row for student name, student Reveiwe name, Mentor name, rough score for quality of peer review, notes
Email Journal Club Reminder for next week- Done
-- include link to Journal Club page
-- include link to the Study Q's (use GDrive link from the file)
---- Dr. B is working on making this file.
10/27/14
Check Peer Review assignments and enter into Google spreadsheet
Check who has now completed the Virtual Screen Refresher (everyone should now have it complete - Vets and Springers)
-- assignment submissions are in GDocs
-- enter onto Google spreadsheet
-- enter grade into Canvas
110314
Check M&M cloning submission - enter onto a Google Spreadsheet if late or not.- Done
Check Wikispaces for Weeks 8,9, 10- Done
Lab hours check for the past week (Week 10) and enter grade for last set Week 8,9 - Done
Journal Club scores from last week-Done
110514
Set due dates for the PeerReview assignments: cloning, virtual, expression - Done
Assign Peer Reviewers for M&M Cloning. - Done
- in Canvas
- see how Grace did the Peer Reviewer Assignments for the Mid Semester Report
- have a strong person review a weaker one
- don't have anyone in the same target review each other
Each Person Reviews 2 different people
- review one springer
- review one veteran
HERE ARE THEIR INSTRUCTIONS
Peer Review of M&M Cloning Due at m/n -
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
11/11/14
receipts and purchasing from the pigeon hole box in lab and putting those in the spreadsheet on GDrive. - Done
- making sure each one is entered, if not enter all the info
- putting a check mark on the paper when it is entered
- then put the receipts in Dr. B's mailbox in the office
11/17/14
enter last Journal Club Study Q's grade into Canvas. Kavya entered the grades into a Gdrive spreadsheet somewhere.- Done
check the M&M Virtual for who has turned theirs in late or on time (was due last night)- Done
Assign mentors to which Notebooks they will review for this weekend (Weeks 11,12,13) -Done
Assign students to Peer Review for M&M Virtual (use Canvas to assign) - have them review a different person, but do the same thing as last time where they each reviewed 2 different people and ideally they get one Springer and one Veteran.
Make an M&M Virtual grading sheet in GDrive (alongside your M&M Cloning one) - Done
Make an M&M ExpressPurChar sheet too- Done
Check which students have done Peer Review for M&M Cloning- Done
- each student had 2 reviews to do
- check lateness
- enter rough score onto GDrive sheet
Assign mentors to review M&M cloning, M&M virtual, M&M ExprPurChar- Done (its in the same folder as the Mid Semester Report)
- use same assignments that they had for the Mid Semester Report
- don't worry about making a column for the mentors to assess the Peer Review - because there were 2 reviews per each. (you are checking these instead)
11/29/14
Final Week Items
HOURS- Need copy of Hours Sheet
Update hours from sheet to Google Drive (Week 13, 14) - Week 15 to be done by Dr. B
Enter hours grades into Canvas
-- double check old Hours grades - some of these were out of order from the paper sheet to the Canvas sheet
Update 6th JClub grades into Canvas from GDrive
On Thursday: Pre-grade 7th JClub Study Q's & Update grades into Canvas
Wikispaces- Done
Create assignments in Canvas for each Wikispaces check (see Schedule to determine which weeks are in each time check) - sort of done by Dr. B
Enter grades for each Wikispaces check
M&Ms- Working
Check which students have turned in late versions of M&M Cloning, M&M Virtual, M&M Exrp,Pur,Char
PEER REVIEWS- Working
Go back and double check which students have done Peer Review for Research report on Target (Mid Semester) (each has 1)
Go back and double check which students have done Peer Review for M&M Cloning (each has 2)
Check which students have done Peer Review for M&M Virtual (each has 2)
- check lateness
- enter rough score
No peer reviews for M&M Expr, Pur, Char (canceled this one)
MISSING/LATE ASSIGNMENTS
Go back and double check for any late/missing assignments (enter score based up on lateness)
PyMol Refresher
Virtual Refresher
pLIC Exercise, etc.
PyMol Image Contest ?
COMPLETED THINGS:
- fix link on Wikispaces menu that goes to the Fall 14 Schedule - DONE
- email entrire class on canvas about new room for Class B - DONE
- upload Syllabus to Wikispaces and link to menu - DONE
- print 30 photorelease forms - DONE
- print 1st journal club article (30 copies, 2 sheets per page, double sided) - DONE
- see if we can get syllabus printed by 2pm? - SKIP
- Upload syllabus to CANVAS and link to front page - DONE - Lab Notebook Grading Rubric
- Embed 'widget' for Fall14 Schedule spreadsheet form Google Docs into Canvas front page
- post fire safety training on the Wikispaces Timeline F14 for that day.
- drop student - DONE
- edit FRI Open House Hours on the VDS Google Website (https://sites.google.com/site/vdsstream/ should be able to login with VDSStaff account for Google)
Open House Hours in general are between Sep 22-Oct 10, 2014 (our specific dates/times will be: M 3-4, T 4-5, F 2-3 - add the specific dates)
-update 1 -page sheet to post in hallway. (Dr. B needs to put in a folder in VDSStaff ......), print and post
- update other 1 page with Dr. Stovall's info. (Dr. B needs to put in a folder in VDSStaff ......), print and post
-- Upload 2014 Posters to the VDS Google Website (poster are in GDrive/posters for the VDSclass Google account)
-- Enter names of each graded assignment into Canvas
-- Upload grades to Canvas (as we get them)
LabNotebook A
- move labnotebooks to another location for those that did not continue VDS (put them at bottom of pigeon holes) -
- update purchasing spreadsheet using receipts in the Pigeon Hole marked 'VDS Receipts'
Use the MentorLabLog on GDocs/VDSstaff for as a Lab Notebook for Wet Lab tasks
NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
Packages: Open, figure out if it is VDS, show to Owais if there, Label appropriately, Place in proper storage, Give receipt to Dr. B and let him know it has arrived and is stored NOTES
- show them Alt + i + t for time stamp in Word
- their files should be stored in their Student folders inGDocs
MENTOR TASKS
TASKS FOR 1st WEEK:
Vicky, Kavya, Anita, Priya - work on the competent cells and the
Take a new set of pictures of the mentors with their names - to put on the this Mentors page. Take groups of 2 or 3 or use individuals. -
schedule mentor meeting -
prepare mentor schedule on GDocs -
prepare student schedule on GDocs -
make a copy of 'hours' chart in GDocs and Archive under new name (Summer) - clear existing Hours chart and add/substract name - SHEET CREATED - just needs names of students
use VDS Mendeley account and upload journal papers -
update VDS google Website and upload this past years posters as PDFs (have Dr. B add you or VDSstaff@gmail as an editor)-
Walk through TDRTargets Exercise - on computer -
Create Weekly Subheadings with correct dates correpsonding to the week: e.g.....
TASKS FOR 2nd WEEK (DATES..????.):
TASKS FOR 3rd WEEK ():
ADMINISTRATIVE/OFFICE WORK
view and revise our lab 'mission statement' - ALL
Please Print, Read and Sign the Mentor Contracts. Then return to Dr. B - ALL --- Mentor Contract on GDocs
update mentor schedules -
update Class Schedule (for mentors not students) -
Know how to do electronic time sheets
post Labnotebook Grading rubric to Wiki (upload PDF then in space.menu on lhs - make link to file) - PRIYA
Create new 'blank' pages on the Research Pages 2014 for each new student. Organize them into Veterans, Springers
Complete the Weeks Layout on the Research Pages page:
In 'Pigeon Holes' for lab notebooks
organize pigeon holes by moving VDS Alums to the other lab notebook stacks -
create and print new hourly sign-in sheet (don't need to do TA though) - see old one in GDocs either VDSStaff or /Mentors
Student Folder:
put new sign in sheet for students (get from Dr. B
make picture roster of students and staff pics (get photo roster from Dr. B - but add in staff pictures)
make Mentor name tags with VDS logo on them
WIKISPACES WORK
create Wikispaces Resesarch pages for each student
ENTER PURCHASING INTO GOOGLE SPREADSHEET FROM SUMMER
-- see receipts in Dr. B's receipts pigeon hole
Lab Safety
Check lab safety completion for all students
-- see the printed sheets in the lab binder and then cross check them to the Wikispaces 'Required Lab Safety' page
- cross reference to UTEIDs of Class Roster (can be found in VDSstaff@gmail.com account
Check Ice Room access list -
LAB WORK
general lab cleaning - ALL
Prep collirollers - split into 2 bottles and rinse then autoclave, then distribute ~6 beads/tube into 600 ul microcentrifuge tubes in a sterile fashion and store in 96well plastic 'brick' in our cubby. -
1 person make a 100 bp ladder (need to have received it from ordering) -
clean pH probe and bottle and replace solution -
Make some Amp plates (~20)
Make some Kan plates (~20)
Make autoclaved water and aliquot several into 1.7 ml centrifuge tube, label and store in -20degC. -
put specs in correct boxes, see if we are missing anything -
Get rid of old LB media and wash bottles -
organize red Sigma Kit boxes (PCR Cleanup, Gel Extraction, Miniprep Kit). Consolidate and then discard all but two boxes for each type: current box and a spare solutions box. -
Organize plates by Staff, vs. Summer, vs etc. -
-- Put contaminated plates in zip locs, put a note on them that they are for disposal, but leave in fridge in a certain spot for the user to dispose of (I want them to see first).
Update Laptops and Desktops -
Start up laptops and do Windows and Browser updates on them. Remove security credentials. -
Clean off old icons from Desktops of Desktop & Laptop computers-
Install both printers on each laptop and each Desktop (see below on this page for instructions) -
TASKS FOR 2nd WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Friday - total students' hours from the sign in sheet and upload to the Hours Column Chart (in the VDSStaff account). Be sure you can see the changes on Wikispaces Hours page -
NOTE ($): When doing Submit to DNA sequencing - we have a NEW account number. Be sure you don't use the old one from last year.
NOTE: newly made plasmids go in the 'Unverified Plasmids' box until they have been verified by DNA Sequencing.
TASKS FOR 3rd WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Test out PyMol Refresher - not posted yet
Test out: Virtual Screen Refresher - (not posted yet
TASKS FOR 4th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
TASKS FOR 5th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Friday - verify Training History pages (paper versions in folder) of Springers. Check of which ones have everything on the Safety page -
use class sign in sheet to see list of all students http://vdsstream.wikispaces.com/Required+Lab+Safety
Test out: LICpNIC-Bsa4cloningExerciseVDS_Fall14.docx -in VDSStaff GDocs/Misc folder - ALL Mentors
TASKS FOR 6th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. -- Mon - prepare 5% sucrose, sterile filtered
-- total lab hours from paper sign in sheets and upload to spreadsheet on GDocs Hours Tues - Wed - journal club grading, add rest of Journal club papers to Mendeley account (vdsclass@gmail.com, you know the password) Thurs
-- verify lab safety training for all students
prepare 5% sucrose, sterile filtered
prepare FPLC - buffer. Make 50 mM Tris, 150 NaCl, pH 8.0 sterile filter, degass see /GDocs/Misc/SolutionsandDilutions
Fri
TASKS FOR 7th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. -- Mon -
Tues -
Wed - add rest of Journal club papers to Mendeley account (vdsclass@gmail.com, you know the password) Thurs Fri
NOTE: for the next Journal Club on the Ricin paper from Dr. Robertus' lab, I have placed an example image of what their PyMol answer for Question #0 should roughly look like. See the handout Q's on the Journal Club page for specifics
in GDocs/VDSStaff/Misc
TASKS FOR 8th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Comments on the Mid-Semester Research Reports assigned to you (~6-7) - in PROGRESS
-- use Canvas' site to do Speed Grader. (collaborative reviews)
Lab Notebook grading (Springers) -
2. Total Hours and enter on spreadsheet GDocs
3. Wikispaces checks and grades
4. LIC cloning Exercise grading
5. Distribute Journal Club papers
TASKS FOR 9th WEEK (Oct 21st - Oct 26th):
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
TASKS FOR 10th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
TASKS FOR 11th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
TASKS FOR 12th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
TASKS FOR 13th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Dilute Compounds - (see Below) - started by Suman
Transform YopH in pNIC-Bsa4 into BL21(DE3) cells - done by Urvashi and Suman
-- NEED to check plates for these and Transfer to 4degC - TUESDAY Mentors do this......
TASKS FOR 14th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
TASKS FOR 15th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Tasks for 15th Week ()
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
M&M'sCheck
M&M Cloning -
M&M Virtual -
M&M Expression, Purification, Characterization -
- determine who has turned them in late (or not at all)
upload to Docs/VDSstaff/Grading_Wiki_LabNotebook_JournalClub_Etc/M&Ms_PeerReviewChecks
At the top row of the spreadsheet are the Due Dates for each assignment
Log In to Canvas course
go to the Grades tab for the each M&M
-- if the box is pink - the assignment was late, click on it to see when the submitted, then enter the # of days late onto the spreadsheet. If they have an excused late - subtract those dates from the total days late.
-- if the box is missing, then type 'missing' and highlight the cell red, enter '100' for # of days late
Peer Reviews check
Peer Review for M&M Cloning -
Peer Review for M&M Virtual
Peer Review for M&M Expression, Purification, Characterization
- login to Canvas
Click on 'Assignments' then on the M&M that you want to take you to the setup page.
- on the right, click on 'Peer Reviews'
Keep this page open on one side of your screen
Then open the other side of your screen with the 'Grades', then for the assignment you want, mouse over the blue name of the assignment until you see a little down arrow - to open 'Speed Grader'
-- verify that the Peer Reviewer has made comments for both of their papers.
-- Just because they have a yellow '!' mark on the Peer Review page, doesn't mean that they haven't done it. Sometime they put them in the 'Discussion' section, sometimes they upload a comments file, and sometimes they are just on the yellow comment boxes on the page.
-- if they did not do one of their reviews type: '0' and make the box red
-- if they did not make enough comments (5 criticisms and 2 compliments) then: give them an appropriate score out of 10.
-- if they could not do their because the other person did not submit - then only grade the one review. But make a note of it somewhere.
OLDER STUFF 11/17/2014 Push them to get their virtual done (control ligands and small libraries at the very least - big library if they want to put in extra effort) Push them to get their cloning - at the minimum, each springer should have two rounds of cloning. If they are strategic - they can do these back-to-back with some overlap. Expression and nickel purification would put them in a much better place.
HIGH PRIORITY: Research Progress Checks Mentors will assess research progress later in the semester. Use spreadsheet in GDrive/VDSStaff http://vdsstream.wikispaces.com/ResearchProgressF14 - only check up to Sunday Nov. 2nd (the last time they did a Wikispaces/Lab Notebook) - I copied the values from last check - update with the current information and see difference in score.
SECOND PRIORITY: Review their M&M Cloning - for this put comments down for improvement and give a rough score. - you will review the same people that you did for the Mid Semester Research report (Eric will make a Google Sheet for this) - don't worry about evaluating the Peer Reviewers work on these (there are two people per - so Eric will check these)
Competent cells - Vicky and Anita PFU Polymerase - Kavya and Priya
MAKE THE VETERANS DO THESE: Dilute new 100 bp ladder in Blue Juice + TE (only a few people) - must use the Solutions&Dilutions Spreadsheet in GDocs to calculate label Q5 polymnerase with date and VDS and store in Top Loading freezer (they are in the Julio now) label BsaI and do the same with it. Label the two new boxes of Oligos (in -20degc Julio now - keep there)
Make LB+Kan plates (10) - ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
Make LB + Kan/Suc plates (30) ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
Mentors, use the MentorLabLog to record research related tasks that you have done so that we can have continuity when passing off a task from one mentor to another e.g. transformations, bacterial cultures, conditions of protein preps, storage conditions, etc.
Weekly Tasks update hours
Set up Pre-meetings for Presenters (email the students to set up times) JOURNAL CLUB PRESENTATIONS (every other week) -- Friday afternoon Pre-meeting with Dr. B + Journal Club people (2) -- Monday or Tuesday afternoon - 2nd Penultimate meeting with Dr. B
TECHNICAL PRESENTATIONS -- Friday afternoon Pre-meeting with Grace + the two presenters -- Monday (or maybe Tuesday) afternoon - 2nd Penultimate meeting with Dr. B
RESEARCH PRESENTATIONS -- Friday afternoon Pre-meeting with Oscar + the two presenters -- Monday (or maybe Tuesday) afternoon - 2nd Penultimate meeting with Dr. B
Tasks for 16th WEEK():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --
Check Wikispaces (use Google Docs Spreadsheet that we have) -
Research Progress spreadsheet updating. In the /VDSStaff/LabHours folder on GDocs
-- LabProgress
-- use Wikispaces and LabNotebooks to determine their progress --
dilute the phosphatase compounds
- to 50 mM in DMSO
- to 5 mM in DMSO/Water
See the instructions diluting compounds in GDocs/Misc/Compounds
Make some 0.01 mM Orthovanadate in water
Make some tubes of 50% water/50% DMSO. Make 20 tubes of 10 ul each in the 0.600 ml tube size ( medium sized micro centrifuge tubes)
Make 20% Sucrose - sterile filtered -
Degass some FPLC buffer - S
Make LB Agar/Kan/Suc plates -
Check Wikispaces (use Google Docs Spreadsheet that we have) -
Research Progress spreadsheet updating. In the /VDSStaff/LabHours folder on GDocs
-- LabProgressAsOf..........
-- use Wikispaces and LabNotebooks to determine their progress --
Verify that students have done their 2 Peer Reviews of other students' M&M Cloning. -
-This is on Canvas.
-Create a new Column in the Wikispaces grading sheet
-Check to see if they have given:
--5 Constructive Criticisms
--2 Compliments
Give 10 pts for a good review, give 9.5 for an ok review, give 9 for a not good review, give 0 for nothing.
Sonicator & Big Centrifuge:
go with the new students when they are doing sonication and big centrifuge. You should go with them unless they have done it 2 times on their own.
Make TGS
-- 500 ml of TGS 5X stock buffer for running gels. See the Spring Buffers&Solutions protocol in the GDocs/Protocols/
Make LB
-- make 2 Liters of LB and keep in bottles in 4degC fridge. Label as "VDS Class" and put a date on it.
Dilute Compounds when they arrive from Chembridge:
Use this Google Docs/Misc/Compounds/instructionsdilutingcompounds for instructions & sheet to do calculations
-- STEP A: Make 50mM Stocks of each compound in 100% DMSO and enter info on the table
-- STEP B: do dilution test of compound in a mixture of DMSO/Water
-- STEP C: Make a final dilution for the students' enzymes assays using the concentration that worked - i.e. was soluble
TASKS FOR 11th WEEK (Nov 4th - Nov 9th):
Wednesday 11/06/13 Need a mentor to find the webpages that have the 'proper' journal paper citations for these resources - i.e. not just a webpage citation. Then list them in Piazza as a post under M&M lablel. PyMol – Schrodinger website has the citation, Cite the original GOLD paper – the 1995 one– see the CCDC website SWISS-MODEL, ICM Molsoft, MolProbity - DONE
Wikispaces checks - complete theses
Lab Notebook checks - (veterans book only)
Test Pfu Polymerase using PCR for pNIC-Bsa4 protocol. -- use Q5 buffer, pLic For and pLic Rev primers
TASKS FOR 10th WEEK (Oct 28th - Nov 2nd):
Tues
make overnight cultures (4 colonies - of FtHAP) in 4 ml of LB - pass of the overnight culture to next mentor
also grow up overnight cultures of Pfu polymerase cells
Wed
Make Glycerol stocks of cultures and store in -80degC (metal basket). Label well.
- see protocol on GDocs for glycerol stocks
grow up Pfu polymerase (obtained from Dr. McDonald), - Daniel, Michael, Andrew
keep notes in MentorLabLog - to record what has been done
AMP plate in Fridge (we think they are BL21(DE3) cells
grow in up in 5ml LB and make glycerol stocks for archival storage
Grow 2 liters in BL21(DE3) and express, purify, characterize - see protocol in VDSStaff GDocs
Test batch of Pfu polymerase - PCR amplify a known target (e.g. pGBR22), or the Sac B gene.
SOLUTIONS INSTRUCTIONS:
(also see the Solutions&Dilutions Spreadsheet on GDocs for help with calculations)
Make LB - 2Liters - and autoclave Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)
(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Printer Installation
Login as Mentor, Start Menu,
Devices And printers
Add New Printer
Add "local" printer
Create New Port --> standard TCP pathway
Enter IP 128.82.195.186
Printer Name Lexmark C543
Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer Name
MENTOR TASKS
11/28/14
After Thanksgiving
Push them to get their virtual done (control ligands and small libraries at the very least - big library if they want to put in extra effort)
Push them to get their cloning - at the minimum, each springer should have two rounds of cloning. If they are strategic - they can do these back-to-back with some overlap.
Expression and nickel purification would put them in a much better place.
Finish Reviewing their M&M Cloning in Canvas - if you have not already done so (should be done already)
- see: GDrive/VDSStaff/Reviewing/PeerReviewAndMidSemesterAssesment by MENTORSandDrB
See Sheet on GDrive, Use VDSstaff login
- for this put comments down for improvement and give a rough score.
- you will review the same people that you did for the Mid Semester Research report (Eric will make a Google Sheet f
or this)
- don't worry about evaluating the Peer Reviewers work on these (there are two people per - so Eric will check these)
Review their M&M Virtual in Canvas (should be completed by Tuesday night)
Use tabs on GDrive sheet to switch between assignments
- for this put comments down for improvement and give a rough score.
- you will review the same people that you did for the Mid Semester Research report (Eric will make a Google Sheet for this)
- don't worry about evaluating the Peer Reviewers' work on these (there are two people per - so Eric will check these)
Research Progress Checks (should be completed by Tuesday night)
Use spreadsheet in GDrive/VDSStaff
http://vdsstream.wikispaces.com/ResearchProgressF14
- only check up to Sunday Nov. 23rd (the last time they did a Wikispaces/Lab Notebook)
- I copied the values from last check - update with the current information and see difference in score.
Review their M&M Expression, Purification, Characterization (should be completed by Friday night)
Thursday/Friday/Saturday - Lab Cleanup days
- they sign up for sheet on the whiteboard
- mentor signs off once done
Monday - VDS Party at Dr. B's House
ULN Interns
Faculty & External Relations Assistant - Bridgitte- see other sheet for tasks
VDS Class Assistant - Eric B
EVERY OTHER WEEK - on Mondays
- check that Wikispaces are done for each student (this will repeat Every other week) (Now may be moving to every 3 weeks - check schedule to verify)
---- put comments on each page
-- upload reviewing score to Google Docs spreadsheet and to Canvas
Lab Notebook (maybe every 2 week or every 3 weeks as determined by the schedule) -Done
- assign mentors to review each (use GDocs/VDSStaff/Reviewing/)
- once Priya has proofs them - upload grades to Canvas
WEEKLY TASKS
Update Hours spreadsheet - Mondays -Done
get paper sign in sheet form lab and enter hours into the spreadsheet on GDocs.
make sure the graph on Wikispaces now shows the latest week - need to update the links on the left most average column
scan sign in sheet and email to Dr. B (or just give the hard copy)
Update Mentors Schedule - ~ onThursdays- Done
create a new sheet within the existing Scheduling Mentors
call it Week XX and move it to the left.
remove all of the 'mentorVDS' blocks under each name and re-color the original colors.
get the link for the page from the 'Share' button and email out to the mentors requesting that they update their conflicts for next week. (one we have that info, we can make new mentor times)
Make New Lab Schedule for WeekX - ~ on Fridays- Done
make new sheet within existing spreadsheet and call it WeekXX
make lab time blocks for each day (put down a time - but we can revise them once you get it up there and we figure out the mentor schedule)
Journal Club reminder emails to class at large when the Journal Paper and the Questions's are posted - on Fridays
-- check the ScheduleFall14 for when Journal Club is
ADDITIONAL FOR WEEK 6:
Fill in ResearchProgressVDS_F14_forStaffGDocs sheet with students' names. -Done
http://vdsstream.wikispaces.com/ResearchProgressF14
Same for:
TargetPageGradesforPostingToGDocsF14
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDluYkhLX3BWbWFtWHQyMnRRakltUlE&usp=sharing
- need to fill in their Target Name Prefixes (can get from the Target spreadsheet):- Done
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDBSNlprOWNxRmdzYnVieGlVc0FSakE&usp=sharing
Next, start looking at each Team's Target pages and marking on the TargetPageGradesforPostingToGDocsF14 whether they have the items or not. This will be part of a grade.- Done
http://vdsstream.wikispaces.com/Targets
Few new things (093014) - Dr B
For the Hours sheet - Done
-- be sure the left most 'Week' column links to the latest week (verify that you can see the latest week on the bar graph on Wikispaces Hours page) - note Zains will always be out of order in the sheet vs Canvas.
-- Upload grades for hours in Green highlight on the Hours page to the Canvas.
ON the Wikispaces Research Pages - Done
- change the order of the link to wach students' page to be alphabetical by last name (with Springers as the first group and Vets as the second group).
- then change order of rows in the Wiki grading spreadsheet in Google Docs to match
(will be easier to review them when in order)
Upload LabNoteB grades to Canvas- Done
New things (10/06/14) - Dr. B
create assignments on Canvas for -Done
PeerRevMidSemResRep
M&M Cloning
PeerRevCloning
M&M Virtual
PeerRevVirtual
M&M ExpressPurChar
PeerRevExpPurChar
100714 - Done
Start entering names and UTEIDs of students from the Open Houses into a spreadsheet on VDSStaff GDrive
put in /Misc folder - call it OpenHouseSignInsVDSF14
The paper list is on the clipboard in the lab. Leave a few sheets there for the Friday Open House
Scan and email copies to me. Can leave originals in my mailbox or on desk.
After Friday open house, enter the rest of the names.
I will send some to the Stream Sort
10/19/14 - Week 9
Using your spreadsheet in GDocs, then upload to Canvas- Done
check to see who has PyMol Refresher done (re-check since the first round not many had turned in).
On your spreadsheet in Google Docs, Enter the date that they submitted (we can adjust grade based on days late).
Enter a Base Grade (assuming no days late)
Assign points late and upload finals to Canvas
.
Lookin GDrive/VDSclass/Results&Data/PyMolRefresher
- if assignment is there and they have the images (compare across the assignments to see what is needed), then they get a 10. If not put a '0' or a fraction of the grade based upon what is missing. I will check the fractional ones.
VETS - should be completed already
SPRINGERS - should be completed already
Using your spreadsheet in GDocs, then upload to Canvas- Done
check to see who has Virtual Screening Refresher done
Make a grade column in Canvas.
Lookin GDrive/VDSclass/Results&Data/VirtualScreeningRefresher
- if assignment is there and they have the Tables and images (compare across the assignments to see what is needed), then they get a 10. If not put a '0' or a fraction of the grade based upon what is missing. I will check the fractional ones.
On your spreadsheet in Google Docs, Enter the date that they submitted (we can adjust grade based on days late).
Enter a Base Grade (assuming no days late)
Assign points late and upload finals to Canvas
VETS - should be completed already
SPRINGERS - check at beginning of next week (Week10)
Upload LabNotebook C grades to Canvas- Done
Check Wikispaces for Week 5,6,7- Done
-- see Schedule for due date
-- upload to Canvas (change grade name in Canvas to be Wiki5,6,7)
Upload grade to Canvas for Target Page Grade- Done
Add sheet for pLIC Cloning Exercise to one of your spreadsheets - Done
- just needs to be graded for completeness (i.e. full credit if all there, or partial for most, or none if missing)
- upload to Canvas
10/23/14
Schedule an Enzyme Assay Meeting with some of the Veterans and Dr. B (and Vicky and Anita)- Done
-- Primary people: Luis, Nikki, Andee, Cidia, Charina, Andrei, Hailey
-------------Secondary People: Zain, Carolyn, Xenia (Brianna), Christ T
-- check students schedules and Dr. Bs
-- shoot for Monday afternoon (~11:30 or 12?) - verify with Dr. B
--- send out email to those people
Modify Grades -Done
-- Monica Li for pLIC cloning exercise - gets a 10 -Done
-- Snaiya Hirani - PyMol Refresher - gets grade according to the date it was created (I think she did it on time - but just had it in her Student folder instead of PyMol Refresher folder)- Done
Create new GDrive spreadsheet in VDSStaff/Reviewing for the Mentors to do Peer Review assessment - Done
- should have a row for student name, student Reveiwe name, Mentor name, rough score for quality of peer review, notes
Email Journal Club Reminder for next week- Done
-- include link to Journal Club page
-- include link to the Study Q's (use GDrive link from the file)
---- Dr. B is working on making this file.
10/27/14
Check Peer Review assignments and enter into Google spreadsheet
Check who has now completed the Virtual Screen Refresher (everyone should now have it complete - Vets and Springers)
-- assignment submissions are in GDocs
-- enter onto Google spreadsheet
-- enter grade into Canvas
110314
Check M&M cloning submission - enter onto a Google Spreadsheet if late or not.- Done
Check Wikispaces for Weeks 8,9, 10- Done
Lab hours check for the past week (Week 10) and enter grade for last set Week 8,9 - Done
Journal Club scores from last week-Done
110514
Set due dates for the PeerReview assignments: cloning, virtual, expression - Done
Assign Peer Reviewers for M&M Cloning. - Done
- in Canvas
- see how Grace did the Peer Reviewer Assignments for the Mid Semester Report
- have a strong person review a weaker one
- don't have anyone in the same target review each other
Each Person Reviews 2 different people
- review one springer
- review one veteran
HERE ARE THEIR INSTRUCTIONS
Peer Review of M&M Cloning Due at m/n -
–You have 2 different people’s which you need to review
–Make 5 constructive criticisms
–Make 2 compliments
- make sure to add your Initials to each comment so we know who did what - JTB
11/11/14
receipts and purchasing from the pigeon hole box in lab and putting those in the spreadsheet on GDrive. - Done
- making sure each one is entered, if not enter all the info
- putting a check mark on the paper when it is entered
- then put the receipts in Dr. B's mailbox in the office
11/17/14
enter last Journal Club Study Q's grade into Canvas. Kavya entered the grades into a Gdrive spreadsheet somewhere.- Done
check the M&M Virtual for who has turned theirs in late or on time (was due last night)- Done
Assign mentors to which Notebooks they will review for this weekend (Weeks 11,12,13) -Done
Assign students to Peer Review for M&M Virtual (use Canvas to assign) - have them review a different person, but do the same thing as last time where they each reviewed 2 different people and ideally they get one Springer and one Veteran.
Make an M&M Virtual grading sheet in GDrive (alongside your M&M Cloning one) - Done
Make an M&M ExpressPurChar sheet too- Done
Check which students have done Peer Review for M&M Cloning- Done
- each student had 2 reviews to do
- check lateness
- enter rough score onto GDrive sheet
Assign mentors to review M&M cloning, M&M virtual, M&M ExprPurChar- Done (its in the same folder as the Mid Semester Report)
- use same assignments that they had for the Mid Semester Report
- don't worry about making a column for the mentors to assess the Peer Review - because there were 2 reviews per each. (you are checking these instead)
11/29/14
Final Week Items
HOURS- Need copy of Hours SheetUpdate hours from sheet to Google Drive (Week 13, 14) - Week 15 to be done by Dr. B
Enter hours grades into Canvas
-- double check old Hours grades - some of these were out of order from the paper sheet to the Canvas sheet
Update 6th JClub grades into Canvas from GDrive
On Thursday: Pre-grade 7th JClub Study Q's & Update grades into Canvas
Wikispaces- Done
Create assignments in Canvas for each Wikispaces check (see Schedule to determine which weeks are in each time check) - sort of done by Dr. B
Enter grades for each Wikispaces check
M&Ms- Working
Check which students have turned in late versions of M&M Cloning, M&M Virtual, M&M Exrp,Pur,Char
PEER REVIEWS- Working
Go back and double check which students have done Peer Review for Research report on Target (Mid Semester) (each has 1)
Go back and double check which students have done Peer Review for M&M Cloning (each has 2)
Check which students have done Peer Review for M&M Virtual (each has 2)
- check lateness
- enter rough score
No peer reviews for M&M Expr, Pur, Char (canceled this one)
MISSING/LATE ASSIGNMENTS
Go back and double check for any late/missing assignments (enter score based up on lateness)
PyMol Refresher
Virtual Refresher
pLIC Exercise, etc.
PyMol Image Contest ?
COMPLETED THINGS:
- fix link on Wikispaces menu that goes to the Fall 14 Schedule - DONE
- email entrire class on canvas about new room for Class B - DONE
- upload Syllabus to Wikispaces and link to menu - DONE
- print 30 photorelease forms - DONE
- print 1st journal club article (30 copies, 2 sheets per page, double sided) - DONE
- see if we can get syllabus printed by 2pm? - SKIP
- Upload syllabus to CANVAS and link to front page - DONE
- Lab Notebook Grading Rubric
- Embed 'widget' for Fall14 Schedule spreadsheet form Google Docs into Canvas front page
- post fire safety training on the Wikispaces Timeline F14 for that day.
- drop student - DONE
- edit FRI Open House Hours on the VDS Google Website (https://sites.google.com/site/vdsstream/ should be able to login with VDSStaff account for Google)
Open House Hours in general are between Sep 22-Oct 10, 2014 (our specific dates/times will be: M 3-4, T 4-5, F 2-3 - add the specific dates)
-update 1 -page sheet to post in hallway. (Dr. B needs to put in a folder in VDSStaff ......), print and post
- update other 1 page with Dr. Stovall's info. (Dr. B needs to put in a folder in VDSStaff ......), print and post
-- Upload 2014 Posters to the VDS Google Website (poster are in GDrive/posters for the VDSclass Google account)
-- Enter names of each graded assignment into Canvas
-- Upload grades to Canvas (as we get them)
- LabNotebook A
- move labnotebooks to another location for those that did not continue VDS (put them at bottom of pigeon holes) -- update purchasing spreadsheet using receipts in the Pigeon Hole marked 'VDS Receipts'
OLDER STUFF
Mentor Info and Tasks:
Calendar for Staff Fall14
Please fill out your weekly schedule here:
https://docs.google.com/spreadsheet/ccc?key=0AsGDXy0cpZridEVGMFJFWHpMMGxYV01lZS1HQ3ZLN1E&usp=sharingg
Use the MentorLabLog on GDocs/VDSstaff for as a Lab Notebook for Wet Lab tasks
NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
Packages: Open, figure out if it is VDS, show to Owais if there, Label appropriately, Place in proper storage, Give receipt to Dr. B and let him know it has arrived and is stored
NOTES
- show them Alt + i + t for time stamp in Word
- their files should be stored in their Student folders inGDocs
MENTOR TASKS
TASKS FOR 1st WEEK:
Vicky, Kavya, Anita, Priya - work on the competent cells and the
Take a new set of pictures of the mentors with their names - to put on the this Mentors page. Take groups of 2 or 3 or use individuals. -
schedule mentor meeting -
prepare mentor schedule on GDocs -
prepare student schedule on GDocs -
make a copy of 'hours' chart in GDocs and Archive under new name (Summer) - clear existing Hours chart and add/substract name - SHEET CREATED - just needs names of students
use VDS Mendeley account and upload journal papers -
update VDS google Website and upload this past years posters as PDFs (have Dr. B add you or VDSstaff@gmail as an editor)-
Walk through TDRTargets Exercise - on computer -
Create Weekly Subheadings with correct dates correpsonding to the week: e.g.....
TASKS FOR 2nd WEEK (DATES..????.):
TASKS FOR 3rd WEEK ():
ADMINISTRATIVE/OFFICE WORK
view and revise our lab 'mission statement' - ALLPlease Print, Read and Sign the Mentor Contracts. Then return to Dr. B - ALL
--- Mentor Contract on GDocs
update mentor schedules -
update Class Schedule (for mentors not students) -
Know how to do electronic time sheets
post Labnotebook Grading rubric to Wiki (upload PDF then in space.menu on lhs - make link to file) - PRIYA
Create new 'blank' pages on the Research Pages 2014 for each new student. Organize them into Veterans, Springers
Complete the Weeks Layout on the Research Pages page:
In 'Pigeon Holes' for lab notebooks
organize pigeon holes by moving VDS Alums to the other lab notebook stacks -organize binders (Student one and Mentor one) -
Mentor Folder:
- print new timesheet pay periods sheet (from UT webpage - Timesheet Pay Periods and Due Dates (see bottom of link)
- create and print new hourly sign-in sheet (don't need to do TA though) - see old one in GDocs either VDSStaff or /Mentors
Student Folder:make Mentor name tags with VDS logo on them
WIKISPACES WORK
ENTER PURCHASING INTO GOOGLE SPREADSHEET FROM SUMMER
-- see receipts in Dr. B's receipts pigeon hole
Lab Safety
Check lab safety completion for all students
-- see the printed sheets in the lab binder and then cross check them to the Wikispaces 'Required Lab Safety' page- cross reference to UTEIDs of Class Roster (can be found in VDSstaff@gmail.com account
Check Ice Room access list -
LAB WORK
general lab cleaning - ALLPrep collirollers - split into 2 bottles and rinse then autoclave, then distribute ~6 beads/tube into 600 ul microcentrifuge tubes in a sterile fashion and store in 96well plastic 'brick' in our cubby. -
1 person make a 100 bp ladder (need to have received it from ordering) -
clean pH probe and bottle and replace solution -
Make some Amp plates (~20)
Make some Kan plates (~20)
Make autoclaved water and aliquot several into 1.7 ml centrifuge tube, label and store in -20degC. -
put specs in correct boxes, see if we are missing anything -
Get rid of old LB media and wash bottles -
organize red Sigma Kit boxes (PCR Cleanup, Gel Extraction, Miniprep Kit). Consolidate and then discard all but two boxes for each type: current box and a spare solutions box. -
Organize plates by Staff, vs. Summer, vs etc. -
-- Put contaminated plates in zip locs, put a note on them that they are for disposal, but leave in fridge in a certain spot for the user to dispose of (I want them to see first).
Update Laptops and Desktops -
TASKS FOR 2nd WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Friday - total students' hours from the sign in sheet and upload to the Hours Column Chart (in the VDSStaff account). Be sure you can see the changes on Wikispaces Hours page -
NOTE ($): When doing Submit to DNA sequencing - we have a NEW account number. Be sure you don't use the old one from last year.
NOTE: newly made plasmids go in the 'Unverified Plasmids' box until they have been verified by DNA Sequencing.
TASKS FOR 3rd WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Test out PyMol Refresher - not posted yet
Test out: Virtual Screen Refresher - (not posted yet
TASKS FOR 4th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --TASKS FOR 5th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Friday - verify Training History pages (paper versions in folder) of Springers. Check of which ones have everything on the Safety page -
use class sign in sheet to see list of all students
http://vdsstream.wikispaces.com/Required+Lab+Safety
Test out: LICpNIC-Bsa4cloningExerciseVDS_Fall14.docx -in VDSStaff GDocs/Misc folder - ALL Mentors
TASKS FOR 6th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Mon - prepare 5% sucrose, sterile filtered
-- total lab hours from paper sign in sheets and upload to spreadsheet on GDocs Hours
Tues -
Wed - journal club grading, add rest of Journal club papers to Mendeley account (vdsclass@gmail.com, you know the password)
Thurs
-- verify lab safety training for all students
prepare 5% sucrose, sterile filtered
prepare FPLC - buffer. Make 50 mM Tris, 150 NaCl, pH 8.0 sterile filter, degass see /GDocs/Misc/SolutionsandDilutions
Fri
TASKS FOR 7th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Mon -
Tues -
Wed - add rest of Journal club papers to Mendeley account (vdsclass@gmail.com, you know the password)
Thurs
Fri
NOTE: for the next Journal Club on the Ricin paper from Dr. Robertus' lab, I have placed an example image of what their PyMol answer for Question #0 should roughly look like. See the handout Q's on the Journal Club page for specifics
in GDocs/VDSStaff/Misc
TASKS FOR 8th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Comments on the Mid-Semester Research Reports assigned to you (~6-7) - in PROGRESS
-- use Canvas' site to do Speed Grader. (collaborative reviews)
Lab Notebook grading (Springers) -
2. Total Hours and enter on spreadsheet GDocs
3. Wikispaces checks and grades
4. LIC cloning Exercise grading
5. Distribute Journal Club papers
TASKS FOR 9th WEEK (Oct 21st - Oct 26th):
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --TASKS FOR 10th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --TASKS FOR 11th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --TASKS FOR 12th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --TASKS FOR 13th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Dilute Compounds - (see Below) - started by Suman
Transform YopH in pNIC-Bsa4 into BL21(DE3) cells - done by Urvashi and Suman
-- NEED to check plates for these and Transfer to 4degC - TUESDAY Mentors do this......
TASKS FOR 14th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --TASKS FOR 15th WEEK ():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Tasks for 15th Week ()
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --M&M's Check
- M&M Cloning -
- M&M Virtual -
- M&M Expression, Purification, Characterization -
- determine who has turned them in late (or not at all)upload to Docs/VDSstaff/Grading_Wiki_LabNotebook_JournalClub_Etc/M&Ms_PeerReviewChecks
At the top row of the spreadsheet are the Due Dates for each assignment
Log In to Canvas course
go to the Grades tab for the each M&M
-- if the box is pink - the assignment was late, click on it to see when the submitted, then enter the # of days late onto the spreadsheet. If they have an excused late - subtract those dates from the total days late.
-- if the box is missing, then type 'missing' and highlight the cell red, enter '100' for # of days late
Peer Reviews check
- login to Canvas
Click on 'Assignments' then on the M&M that you want to take you to the setup page.
- on the right, click on 'Peer Reviews'
Keep this page open on one side of your screen
Then open the other side of your screen with the 'Grades', then for the assignment you want, mouse over the blue name of the assignment until you see a little down arrow - to open 'Speed Grader'
-- verify that the Peer Reviewer has made comments for both of their papers.
-- Just because they have a yellow '!' mark on the Peer Review page, doesn't mean that they haven't done it. Sometime they put them in the 'Discussion' section, sometimes they upload a comments file, and sometimes they are just on the yellow comment boxes on the page.
-- if they did not do one of their reviews type: '0' and make the box red
-- if they did not make enough comments (5 criticisms and 2 compliments) then: give them an appropriate score out of 10.
-- if they could not do their because the other person did not submit - then only grade the one review. But make a note of it somewhere.
OLDER STUFF
11/17/2014
Push them to get their virtual done (control ligands and small libraries at the very least - big library if they want to put in extra effort)
Push them to get their cloning - at the minimum, each springer should have two rounds of cloning. If they are strategic - they can do these back-to-back with some overlap.
Expression and nickel purification would put them in a much better place.
HIGH PRIORITY:
Research Progress Checks
Mentors will assess research progress later in the semester. Use spreadsheet in GDrive/VDSStaff
http://vdsstream.wikispaces.com/ResearchProgressF14
- only check up to Sunday Nov. 2nd (the last time they did a Wikispaces/Lab Notebook)
- I copied the values from last check - update with the current information and see difference in score.
SECOND PRIORITY:
Review their M&M Cloning
- for this put comments down for improvement and give a rough score.
- you will review the same people that you did for the Mid Semester Research report (Eric will make a Google Sheet for this)
- don't worry about evaluating the Peer Reviewers work on these (there are two people per - so Eric will check these)
Competent cells - Vicky and Anita
PFU Polymerase - Kavya and Priya
MAKE THE VETERANS DO THESE:
Dilute new 100 bp ladder in Blue Juice + TE (only a few people) - must use the Solutions&Dilutions Spreadsheet in GDocs to calculate
label Q5 polymnerase with date and VDS and store in Top Loading freezer (they are in the Julio now)
label BsaI and do the same with it.
Label the two new boxes of Oligos (in -20degc Julio now - keep there)
Make LB+Kan plates (10) -
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
Make LB + Kan/Suc plates (30)
ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
Mentors, use the MentorLabLog to record research related tasks that you have done so that we can have continuity when passing off a task from one mentor to another
e.g. transformations, bacterial cultures, conditions of protein preps, storage conditions, etc.
Weekly Tasks
update hours
Set up Pre-meetings for Presenters (email the students to set up times)
JOURNAL CLUB PRESENTATIONS (every other week)
-- Friday afternoon Pre-meeting with Dr. B + Journal Club people (2)
-- Monday or Tuesday afternoon - 2nd Penultimate meeting with Dr. B
TECHNICAL PRESENTATIONS
-- Friday afternoon Pre-meeting with Grace + the two presenters
-- Monday (or maybe Tuesday) afternoon - 2nd Penultimate meeting with Dr. B
RESEARCH PRESENTATIONS
-- Friday afternoon Pre-meeting with Oscar + the two presenters
-- Monday (or maybe Tuesday) afternoon - 2nd Penultimate meeting with Dr. B
Tasks for 16th WEEK():
Total Lab hours and enter onto spreadsheet on GDocs, put Lab Hours sheet in Dr. B's 'reserved' cubby when done. --Check Wikispaces (use Google Docs Spreadsheet that we have) -
Research Progress spreadsheet updating. In the /VDSStaff/LabHours folder on GDocs
-- LabProgress
-- use Wikispaces and LabNotebooks to determine their progress --
dilute the phosphatase compounds
- to 50 mM in DMSO
- to 5 mM in DMSO/Water
See the instructions diluting compounds in GDocs/Misc/Compounds
Make some 0.01 mM Orthovanadate in water
Make some tubes of 50% water/50% DMSO. Make 20 tubes of 10 ul each in the 0.600 ml tube size ( medium sized micro centrifuge tubes)
Make 20% Sucrose - sterile filtered -
Degass some FPLC buffer - S
Make LB Agar/Kan/Suc plates -
Check Wikispaces (use Google Docs Spreadsheet that we have) -
Research Progress spreadsheet updating. In the /VDSStaff/LabHours folder on GDocs
-- LabProgressAsOf..........
-- use Wikispaces and LabNotebooks to determine their progress --
Verify that students have done their 2 Peer Reviews of other students' M&M Cloning. -
-This is on Canvas.
-Create a new Column in the Wikispaces grading sheet
-Check to see if they have given:
--5 Constructive Criticisms
--2 Compliments
Give 10 pts for a good review, give 9.5 for an ok review, give 9 for a not good review, give 0 for nothing.
Sonicator & Big Centrifuge:
go with the new students when they are doing sonication and big centrifuge. You should go with them unless they have done it 2 times on their own.
Make TGS
-- 500 ml of TGS 5X stock buffer for running gels. See the Spring Buffers&Solutions protocol in the GDocs/Protocols/
Make LB
-- make 2 Liters of LB and keep in bottles in 4degC fridge. Label as "VDS Class" and put a date on it.
Dilute Compounds when they arrive from Chembridge:
Use this Google Docs/Misc/Compounds/instructionsdilutingcompounds for instructions & sheet to do calculations
-- STEP A: Make 50mM Stocks of each compound in 100% DMSO and enter info on the table
-- STEP B: do dilution test of compound in a mixture of DMSO/Water
-- STEP C: Make a final dilution for the students' enzymes assays using the concentration that worked - i.e. was soluble
TASKS FOR 11th WEEK (Nov 4th - Nov 9th):
Wednesday 11/06/13Need a mentor to find the webpages that have the 'proper' journal paper citations for these resources - i.e. not just a webpage citation. Then list them in Piazza as a post under M&M lablel.
PyMol – Schrodinger website has the citation, Cite the original GOLD paper – the 1995 one– see the CCDC website
SWISS-MODEL, ICM Molsoft, MolProbity - DONE
Wikispaces checks - complete theses
Lab Notebook checks - (veterans book only)
Test Pfu Polymerase using PCR for pNIC-Bsa4 protocol.
-- use Q5 buffer, pLic For and pLic Rev primers
TASKS FOR 10th WEEK (Oct 28th - Nov 2nd):
Tuesmake overnight cultures (4 colonies - of FtHAP) in 4 ml of LB - pass of the overnight culture to next mentor
also grow up overnight cultures of Pfu polymerase cells
Wed
Make Glycerol stocks of cultures and store in -80degC (metal basket). Label well.
- see protocol on GDocs for glycerol stocks
grow up Pfu polymerase (obtained from Dr. McDonald), - Daniel, Michael, Andrew
keep notes in MentorLabLog - to record what has been done
AMP plate in Fridge (we think they are BL21(DE3) cells
grow in up in 5ml LB and make glycerol stocks for archival storage
Grow 2 liters in BL21(DE3) and express, purify, characterize - see protocol in VDSStaff GDocs
Test batch of Pfu polymerase - PCR amplify a known target (e.g. pGBR22), or the Sac B gene.
SOLUTIONS INSTRUCTIONS:
(also see the Solutions&Dilutions Spreadsheet on GDocs for help with calculations)Make LB - 2Liters - and autoclave
Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Printer Installation
- Login as Mentor, Start Menu,
- Devices And printers
- Add New Printer
- Add "local" printer
- Create New Port --> standard TCP pathway
- Enter IP 128.82.195.186
- Printer Name Lexmark C543
- Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer NamePrinter Name: Lexmark C543 IP: 128.83.195.186
Printer Name: Dell IP: 129.116.152.49
MentorsSp13 (last year's mentors page)
M 3-4, T 4-5, F 2-3